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PLINK data missing for test_regenie datasets

Open gagank1 opened this issue 3 years ago • 1 comments

The README in validation says the datasets used in test_regenie were generated via Hail and stored as PLINK files. We need these original PLINK files to run Glow and validate Regenie results for LOCO association testing. @EpiSlim

gagank1 avatar Jul 07 '21 17:07 gagank1

Hey @gagank1, that data can be generated by following the instructions at https://github.com/pystatgen/sgkit/tree/main/validation/gwas/docker and then https://github.com/pystatgen/sgkit/tree/main/validation/gwas/method/regenie.

It generates these PLINK files: regenie_simulations.zip

eric-czech avatar Jul 07 '21 18:07 eric-czech

Closing as this has been addressed

tomwhite avatar Jan 04 '23 16:01 tomwhite